Table 1 - A table showing the GOLD docking scores of the top 16 ligands from the virtual screening of PP2Ctg with calcium ions in the active site.
Table 2 - A table showing the GOLD docking scores of the top 16 ligands from the virtual screening of PP2Ctg without calcium ions in the active site.
Week 8 - Nothing. Too Many Tests... Week 7 - PP2Ctg Virtual Screening & Lab Report
Table 1 - A table showing information on the top ten ligands from the preliminary virtual screening.
Figure 1 - Part of the first page from my research report.
Week 6 - PP2Ctg Virtual Screening & Protein Expression
Figure 1 - An image from PyMOL showing the 3D structure of three aggregated identical chains of PP2Ctg. The active sites are shown as sticks.
Figure 2 - An image from PyMOL comparing the overlapping active sites of PP2Cα (carbon green) and PP2Ctg (carbon cyan). It includes the names and numbers of the residues (PP2Cα – black, PP2Ctg – white).
Figure 3 - An image of the plate containing the successfully transformed BL21 strain of E. coli that will be used for protein expression.
Week 5 - Virtual Screening Refresher - looks good - Dr. B. any wet lab data?
Table 1 - A table generated from the best ranking list from GOLD showing the top ten ligands from the virtual screening in descending order.
Table 2 - A table showing the top three ligands determined by GOLD including their data related to Lipinski's rule of five in descending order.
Figure 1 - An image showing the docking poses and polar contacts of the top ten ligands as determined by GOLD from left to right and then descending order.
All the top ten ligands determined by gold have long structures of aromatic rings joined by carbon chains, allowing them to position themselves in a bent conformation inside the active site. The cyclic rings seem to contribute to the molecules’ general compatibility with the shape of the active site. The inclusion of a substituent midway through the carbon chain seems to act as a sort of anchoring tail, allowing the molecules to create an additional bond with a residue in the middle of the active site that lies a little further than the others away from the bulk of the molecules’ structures. These purine/pyrimidine-like rings most likely play a large part in the binding of the ligands, which corresponds with the known function of the protein, which includes the manufacturing of molecules later used to create nucleotides. The ability to donate one hydrogen and accept three hydrogens in order to create hydrogen bonds holds true for the top three ligands, possibly leading to the conclusion that the active site has an identical reverse ability to make hydrogen bonds. The three top ligands, according to the Lipinski’s Rule of Five, have promise for medical applications.
Week 4 - Version 3 Transformation and Mini-Prep Processing for Sequencing.
Figure 1 - An image of my attempt to transform E. coli with the plasmid including my CDS from ligation independent cloning. This plate shows four colonies, three of which I grew up and extracted their plasmids for sequencing.
Figure 2 - An image of my attempt to transform E. coli with the plasmid including my CDS from ligation independent cloning. This plate shows no colonies.
Figure 3 - A compilation of the four nanodrop readings I took from the elution from the mini-prep plasmid extraction of sample 2.
Figure 4 - A compilation of the four nanodrop readings I took from the elution from the mini-prep plasmid extraction of sample 3.
Figure 5 - A compilation of the four nanodrop readings I took from the elution from the mini-prep plasmid extraction of sample 4.
Week 3 Nanodrop Deduced Concentrations of CDS for Version 3 and PyMOL Refresher
Figure 1 - An image of the four readings obtained from the Nanodrop spectrophotometer used to determine the concentration of my CDS in solution for version 3 ligation-independent cloning into pNIC-Bsa4. The average was 542.425 ng/ul.
Figure 2 - A compilation of all the images I generated in PyMOL while following the PyMOL Refresher protocol.
Week 2 - Primer Overlap PCR and Cutting of Pnic-Bsa4 for Version 3
Figure 1 - After I completed my PCR overlap, this time including the leading and lagging primers for ligation-independent cloning, I verified its success by running the gel above. Lane 1 - 100 bp ladder. Lane 2 - Primary PCR. Lane 3 - Secondary PCR.
After cutting my accepting vector, pNIC-Bsa4, with BsaI, I verified its succes via the gel above. Lane 1 - 1 kbp ladder. Lane 2 - Uncut pNIC-Bsa4. Lane 3 - Cut pNIC-Bsa4.
Justin's Research
Week 9 - Virtual Screening & Protein Expression
Week 8 - Nothing. Too Many Tests...
Week 7 - PP2Ctg Virtual Screening & Lab Report
Week 6 - PP2Ctg Virtual Screening & Protein Expression
Week 5 - Virtual Screening Refresher - looks good - Dr. B. any wet lab data?
All the top ten ligands determined by gold have long structures of aromatic rings joined by carbon chains, allowing them to position themselves in a bent conformation inside the active site. The cyclic rings seem to contribute to the molecules’ general compatibility with the shape of the active site. The inclusion of a substituent midway through the carbon chain seems to act as a sort of anchoring tail, allowing the molecules to create an additional bond with a residue in the middle of the active site that lies a little further than the others away from the bulk of the molecules’ structures. These purine/pyrimidine-like rings most likely play a large part in the binding of the ligands, which corresponds with the known function of the protein, which includes the manufacturing of molecules later used to create nucleotides. The ability to donate one hydrogen and accept three hydrogens in order to create hydrogen bonds holds true for the top three ligands, possibly leading to the conclusion that the active site has an identical reverse ability to make hydrogen bonds. The three top ligands, according to the Lipinski’s Rule of Five, have promise for medical applications.
Week 4 - Version 3 Transformation and Mini-Prep Processing for Sequencing.
Week 3 Nanodrop Deduced Concentrations of CDS for Version 3 and PyMOL Refresher
Week 2 - Primer Overlap PCR and Cutting of Pnic-Bsa4 for Version 3
Week 1 - Nothing